The longest season has its reward. Chelsea's campaign has taken in 68 matches in 11 different countries across eight competitions, an energy-sapping schedule overseen by two managers that, courtesy of a stoppage-time winner near its end, has yielded silverware. Rafael Benítez paced his technical area here, hands sunk deep into his pockets, as this contest played out its frantic last seconds before the final whistle brought relief.

His punch of the air was stifled by Christophe Lollichon's bear-hug. Once he had emerged from the goalkeeping coach's embrace, there was a smile of satisfaction plastered across his face.

Some measure of the calm professionalism that has typified much of his seven months at Stamford Bridge, one acrimonious evening on Teesside aside, swiftly returned as he busied himself consoling distraught Benfica players. Benítez actually had to be coaxed from his thoughts, as he surveyed his team's guard of honour, to lead the victors up the steps to accept the trophy in the cluttered presentation box.

There were even congratulations from some Chelsea fans as he made that plod up the stairs, and further hugs of gratitude from Michael Emenalo, Ron Gourlay, Dave Barnard and Bruce Buck before he sidled off stage right. He has had to wait some time to receive public thanks for his endeavours at this club. "It has not been easy," he said, "so I am really pleased, really proud."

Proper acceptance at Chelsea was always going to elude the Spaniard, for all the giddy scenes in the aftermath. Theirs has been a fraught marriage of convenience, born of the team's mid-season lull in form and an out-of-work manager's desire to reestablish his credentials away from mere blogs and coaching seminars. He will depart this club in a few weeks' time, once his side have conducted a two-match post-season tour of the United States, with his reputation enhanced within the game. The Europa League has partly helped achieve that. A top-four finish is arguably even more impressive.

But his quiet dignity in an awkward and, from the start, distinctly fractious situation has been admirable. He deserved his chance to hoist the trophy in the aftermath, though the look on his face as he did so betrayed a man who felt he was intruding on someone else's party.

A penny for his thoughts as he held the Europa League aloft and those in the Chelsea end chorused in celebration as they waved their plastic blue flags. Once Sunday's visit of Everton concludes an English club's most cluttered campaign since Arsenal played 70 times in 1979-80, Benítez, will look back with some satisfaction at all he has achieved here. This had been an exercise in short-term firefighting, a lesson in pragmatic survival amid that draining schedule.

Coaching the European champions was not supposed to be a difficult proposition but this was a club with its own particular problems when he succeeded Roberto Di Matteo in the autumn. Chelsea were third at the time, and only four points from the top, but the team's trajectory was clear. They had shipped 21 goals in nine matches, had failed to win in four league games, and the manager who had claimed the Champions League six months earlier was showing no signs of restoring on-field discipline.

The Spaniard has pointed, with some justification, to the imbalanced squad he inherited with Chelsea having overloaded on creative midfielders, all mouth-watering talents but each set upon scuttling runs upfield with little regard for the acres they left unguarded at the back. They boasted only Fernando Torres up front, a player whose form had been flimsy at best.

It is to the interim's credit that the Spaniard's fine goal in the Amsterdam ArenA – the strength and pace of old to flummox Luisão and convert calmly beyond Artur – was his ninth in Europe this term, and only Cristiano Ronaldo and Robert Lewandowski boast more. The Spaniard is a reigning World Cup, European Championship, European Cup and Europa League winner which, in itself, is remarkable.

Benítez had still wanted to add more than just Demba Ba to the ranks in January, with his pleas for a mobile central midfielder falling on deaf ears. Benfica exposed his side's limitations with their fluid, attacking movement, with Nicolás Gaitán, Enzo Pérez and Eduardo Salvio gliding beyond blue-shirted markers far too easily. Chelsea can labour in central midfield when the ball buzzes around them at pace, and at the back when slippery opponents strike an upbeat rhythm. Yet this group retains its stubborn streak, that old refusal to wilt. They clung to the contest, just as they had against Bayern Munich a year ago, and prevailed at the last. A team who has played this many games this term has no right to conjure a 93rd-minute winner when they have been chasing the ball for long periods.

His insistence on juggling his squad, sometimes amid a clamour of criticism, has helped meet his principal objectives. Retaining a level of freshness and zest represented a colossal challenge and, despite the near-misses in domestic cup competitions and the Fifa Club World Cup, he can now point to a significant trophy and Champions League qualification as evidence of proper success.

As his players celebrated raucously on the turf, the blue confetti still drifting around the arena, Benítez held the trophy up to the support once more and was greeted, perhaps for the first time in his short association with the club, with cheers. "I could see everyone was happy," he said. "So I was happy too." This relationship will end well.